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- PDB-2ywj: Crystal structure of uncharacterized conserved protein from Metha... -

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Basic information

Entry
Database: PDB / ID: 2ywj
TitleCrystal structure of uncharacterized conserved protein from Methanocaldococcus jannaschii
ComponentsGlutamine amidotransferase subunit pdxT
KeywordsTRANSFERASE / Uncharacterized conserved protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


pyridoxine metabolic process / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / L-glutamine catabolic process / glutaminase / glutaminase activity / cytosol
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxT
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsManzoku, M. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: to be published
Title: Crystal structure of uncharacterized conserved protein from Methanocaldococcus jannaschii
Authors: Manzoku, M. / Ebihara, A. / Yokoyama, S. / Kuramitsu, S.
History
DepositionApr 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamine amidotransferase subunit pdxT


Theoretical massNumber of molelcules
Total (without water)20,6271
Polymers20,6271
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.816, 50.470, 70.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glutamine amidotransferase subunit pdxT / Uncharacterized conserved protein / glutamine amidotransferase glutaminase subunit pdxT


Mass: 20627.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q59055, EC: 2.6.-.-
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG400, 100MM HEPES, 30% 1,2-propanediol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 9, 2006
RadiationMonochromator: SI Double-Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 13130 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 22.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 7.44 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.51 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1093376 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1350 10.3 %RANDOM
Rwork0.183 ---
obs0.183 13088 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.452 Å2 / ksol: 0.339247 e/Å3
Displacement parametersBiso mean: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å20 Å20 Å2
2---1.58 Å20 Å2
3----0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.9→33.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 0 147 1583
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.211 239 11.3 %
Rwork0.179 1882 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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